[gmx-users] Re: Potential energy from a previous configuration mismatch

[Mark Abraham]

Thanks. http://redmine.gromacs.org/issues/1053 created.

Mark

On Fri, Nov 30, 2012 at 5:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/30/12 11:00 AM, Mark Abraham wrote:
>
>> On Fri, Nov 30, 2012 at 2:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 11/30/12 8:21 AM, escajarro wrote:
>>>
>>>  I do have constraints, all the bond lengths are fixed and they are
>>>> specified
>>>> in the topology file. Am I doing something wrong? I copy here the
>>>> definition
>>>> of one of the models I use. I also tried using in the input the line:
>>>>
>>>> constraints              = all-bonds
>>>>
>>>> instead of
>>>>
>>>> constraints              = none
>>>>
>>>> with the same result
>>>>
>>>> <http://gromacs.5086.n6.**nabb**le.com/file/n5003394/****Clipboard.jpg<http://nabble.com/file/n5003394/**Clipboard.jpg>
>>>> <http://gromacs.**5086.n6.nabble.com/file/**n5003394/Clipboard.jpg<http://gromacs.5086.n6.nabble.com/file/n5003394/Clipboard.jpg>
>>>> >
>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>  That all looks fine, and the results should be the same under those two
>>> circumstances.  The problem is likely due to the fact that L-BFGS cannot
>>> actually make use of constraints (a bug in mdrun), so that is the source
>>> of
>>> the difference.  The EM is being done without constraints, and then the
>>> MD
>>> starts with constraints.  Use a different EM algorithm and see if the
>>> outcome improves.
>>>
>>
>>
>> If L-BFGS is silently not using the constraints, then I think that is a
>> real bug and it would be good to report it so we might sometime fix it. Or
>> maybe it's an undocumented "feature" we need to document? Which is it,
>> please?
>>
>>
> From the recent discussion, it seems that L-BFGS is silently ignoring the
> constraints, as Berk observed there is no check for this combination, which
> explained David's finding that bond lengths seem to vary randomly:
>
> http://lists.gromacs.org/**pipermail/gmx-developers/2012-**
> November/006433.html<http://lists.gromacs.org/pipermail/gmx-developers/2012-November/006433.html>
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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